• Biotechnology
  • Molecular Biology  and Genetics
  • Immunology and Stem Cell Biology
  • Protein Engineering
  • Systems Biology
  • Metabolic Engineering
  • Computational Biology
  • Bioinformatics

Faculty Member, PhD. Ozgur Gul

Project Title: Analysis of ethanol production using consolidated bioprocessing of cellulose using Kluyveromyces marxianus displaying cellulosome
Support: TUBITAK 3501 215Z299
Duration: 2016-2019
Role: Principle Investigator 

Project Title:  Paper-based piezoresistive MEMS biosensor to detect aflatoksin chemical
Support: TUBITAK 3501 117E236
Duration: 2018-2021
Role: Researcher

Faculty Member, PhD. Hilal Taymaz Nikerel

My research interest mainly includes understanding the function and regulation of complex biological processes using systems biology approaches. Quantification of the cellular mechanisms is crucial to engineer the microorganism and to optimize the growth conditions, taking physiological, kinetic and thermodynamic constraints into account. So far I have focused on metabolomics, fluxomics, transcriptomics and their non-linear interactions within the cell, to understand highly complex systems. Such different levels of –omics data were integrated through genome-wide models to understand the effect of various interventions (e.g. drug, substrate perturbation(s), genetic modifications) on the metabolism. My current work focuses on to further extend and incorporate these tools to other –omic levels, covering interactomics and/or proteomics. Such an attempt requires theoretical methods, e.g. building predictive mathematical models, in addition to the experimental efforts, using multidisciplinary advances.

TUBITAK 2232 (Proje No. 114C062), Project Title: Investigation of intracellular effects of chemotherapeutic drugs using systems biology approaches and genome-wide models, 2014-2016 (Principal Investigator).

NCSB (Netherlands Consortium for Systems Biology) - NBIC (Netherlands Bioinformatics Centre), Project Title: Computational modeling approaches and fluxomics, 2010-2012 (Postdoctoral Researcher).

Faculty Member, PhD. Ozlem Ulucan Acan

Dr. Ulucan uses molecular modeling techniques to study structure, dynamics, energetics and interactions of biomolecules. Structural and energetic aspects of protein-protein and protein-small molecule complexes together with computer-aided drug design consist of an important part of her research. Additionally, she is interested in genomic and transcriptomic data analysis and disease subtyping using statistical learning approaches.

Project title: Quantifying allosteric effects in PDK1
This is a joint project with Prof. Dr. Volkhard Helms (Center for Bioinformatics, Saarland University) and Dr. Matthias Engel (Pharmaceutical and Medicinal Chemistry, Saarland University).

Project title: Anticancer drug design by targeting repressive immune checkpoints
In this project we employ computational methods to target the interaction between negative immune check point receptors and their ligands by designing small molecules that bind effectively and specifically to the immune checkpoint ligands.

Project title: Subtyping Gastric Cancer
Gastric cancer is the fifth most common malignancy and the third leading cause of cancer death worldwide (723,000 deaths, 8.8% of the total). Like other types of cancer, gastric cancer is a highly heterogeneous malignancy that arises from a multitude of genetic and epigenetic alterations. In this project, we are aiming at finding the subtypes of gastric cancer, which is important to better identify effective therapeutic strategies. 


Faculty Member, PhD. Sesil Çınar

Her research area is mainly based on computational biochemistry and organic chemistry. Modeling the biochemical reactions to investigate the protein-ligand interactions and their mechanisms; investigation of stereoselectivities in biochemical and organic reactions; synthesis of photoinitiators for dental applications; determination of degradation mechanisms of drug molecules; establishing structure-activity relationship for drug-like molecules, are couple of topics that she has worked on.

Ongoing projects:
Mechanistic study on the catalytic mechanism of protein arginine deiminase 2 (PAD2) (Researcher)

Faculty Member, PhD Ali Deniz Dalgıç

Dr. Ali Deniz Dalgıç's research areas can be classified under two main headings as tissue engineering and controlled drug delivery systems. Research on tissue engineering applications includes the steps of designing and manufacturing innovative scaffolds and the characterization of scaffold properties. His research to date includes the production of cell carriers for bone, ligament, and skin tissue engineering. Some of the basic techniques used in these studies are as follows: production of micro-nano fiber by various electrospinning methods, the design and production of 3D polymer scaffolds, production of ion-doped hydroxyapatite, and bone cement for bone tissue engineering. Regenerative drug loading and release properties are also investigated in the manufactured scaffolds. Studies on controlled drug delivery systems include targeted liposome drug delivery systems and micro-nanosphere drug delivery systems. In these studies, drug-loaded liposome and sphere carriers are produced, combined with targeting agents, and the interaction of the characterized systems with target cells is investigated. In this context, studies have been conducted on targeted/untargeted anti-cancer drug delivery systems and drug systems developed for transport through the blood-brain barrier.

Faculty Member, PhD. Gülşah Gül

Dr. Gül’s research focuses on computational drug design and delivery, the structure-to-property prediction of nano-biomaterials, and molecular modeling and simulation of soft material systems. Some of her current interests are driven by the applications of nanoparticles, polymers and proteins in health and sustainability areas. In this context, the goal is to understand intracellular signaling, cellular uptake, and toxicity mechanisms by examining the interaction and self-assembly behavior of small molecules among themselves and with lipid bilayers. Theoretical studies are complemented by experiments conducted in-house or through external collaborations.